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change from proof reading of Ballon manager docs
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Fixes bug: 3352
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@jonalv
jonalv committed Sep 25, 2012
1 parent 05977db commit 6784af1
Showing 1 changed file with 39 additions and 40 deletions.
79 changes: 39 additions & 40 deletions ...ns/net.bioclipse.balloon.business/src/net/bioclipse/balloon/business/IBalloonManager.java
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Expand Up @@ -25,7 +25,11 @@
import org.eclipse.core.runtime.IProgressMonitor;


@PublishedClass( "Contains methods related to Balloon")
@PublishedClass( "Balloon is a software that creates 3D atomic coordinates. " +
"This manager provides methods for generating 3D " +
"coordinates using Balloon in a few different ways. More " +
"information can be found at: " +
"http://web.abo.fi/~mivainio/balloon/index.php")
/**
* An interface for a Bioclipse Manager for invoking Balloon
* (http://web.abo.fi/~mivainio/balloon/index.php)
Expand All @@ -45,9 +49,9 @@ public interface IBalloonManager extends IBioclipseManager {
@Recorded
@PublishedMethod(
params = "String inputfile",
methodSummary = "Generated 3D coodrinates for all molecules in the " +
"inputfile. Creates a default output file. Inputs: " +
"inputfile = path to inputfile.")
methodSummary = "Generates 3D coodrinates for all molecules in the " +
"inputfile. Creates a default output file with _3d " +
"added.")
String generate3Dcoordinates( String inputfile ) throws BioclipseException;

/**
Expand All @@ -61,9 +65,8 @@ public interface IBalloonManager extends IBioclipseManager {
*/
@PublishedMethod(
params = "String inputfile, String outputfile",
methodSummary = "Generated 3D coodrinates for all molecules in the " +
"inputfile and saves to outputfile Inputs: inputfile " +
"= path to inputfile, outputfile = path to outputfile")
methodSummary = "Generates 3D coordinates for all molecules in the " +
"inputfile and saves to outputfile")
@Recorded
String generate3Dcoordinates( String inputfile, String outputfile )
throws BioclipseException;
Expand All @@ -76,12 +79,11 @@ String generate3Dcoordinates( String inputfile, String outputfile )
*/
@PublishedMethod(
params = "List<String> inputfiles",
methodSummary = "Generate 3D coordinates for all molecules in a list " +
"of inputfiles. Creates a default output file. " +
"Inputs: inputfiles = list of Strings with paths " +
"to inputfiles" )
methodSummary = "Generates 3D coordinates for all molecules in all " +
"files in inputFiles and stores them to a default " +
"output file." )
@Recorded
List<String> generate3Dcoordinates( List<String> inputfiles)
List<String> generate3Dcoordinates( List<String> inputFiles)
throws BioclipseException;

/**
Expand All @@ -93,10 +95,9 @@ List<String> generate3Dcoordinates( List<String> inputfiles)
*/
@PublishedMethod(
params = "List<String> inputfiles, int numConformations",
methodSummary = "Generate 3D conformations for all molecules in a " +
"list of inputfiles. inputfiles = list of Strings " +
"with paths to inputfiles, numConformations = number " +
"of conformations to generate per molecule." )
methodSummary = "Generate numConformations number of 3D " +
"conformations for each molecule in all files in " +
"inputFiles and return them in a List.")
@Recorded
List<String> generate3Dconformations( List<String> inputfiles,
int numConformations)
Expand All @@ -111,12 +112,11 @@ List<String> generate3Dconformations( List<String> inputfiles,
*/
@PublishedMethod(
params = "String inputfile, int numConformations",
methodSummary = "Generate 3D conformations for all molecules in an " +
"inputfile. Creates a default output filename. " +
"inputfile = paths to inputfile, numConformations " +
"= number of conformations to generate per molecule." )
methodSummary = "Generates 3D conformations for all molecules in " +
"the file inputfile and stores them in a file and " +
"returns the name of the created file." )
@Recorded
String generate3Dconformations( String inputfile, int numConformations )
public String generate3Dconformations( String inputfile, int numConformations )
throws BioclipseException;

/**
Expand All @@ -131,39 +131,39 @@ String generate3Dconformations( String inputfile, int numConformations )
*/
@PublishedMethod(
params = "String inputfile, String outputfile, int numConformations",
methodSummary = "Generated 3D conformations for all molecules " +
"in the inputfile. \n" +
"Inputs: inputfile = path to inputfile, outputfile " +
"= path to outputfile, numConformations = number of " +
"conformations to generate per molecule.")
methodSummary = "Generates 3D conformations for all molecules " +
"in the file inputfile and stores them in a file " +
"and returns the name of the created file." )
@Recorded
String generate3Dconformations( String inputfile,
String outputfile,
int numConformations )
public String generate3Dconformations( String inputfile,
String outputfile,
int numConformations )
throws BioclipseException;


@PublishedMethod(
params = "IMolecule molecule",
methodSummary = "Return a new molecule with 3D " +
methodSummary = "Returns a new molecule with 3D " +
"coordinates generated by Balloon.")
@Recorded
public ICDKMolecule generate3Dcoordinates( IMolecule molecule )
throws BioclipseException;

@PublishedMethod(
params = "IMolecule molecule, int numConf",
methodSummary = "Return a list of molecule with selected " +
"number of target 3D " +
"conformations generated by Balloon.")
methodSummary = "Returns a list of molecules with " +
"numConf number of 3D confirmations " +
"generated by Balloon for the given " +
"molecule.")
@Recorded
public List<ICDKMolecule> generate3Dconformations( IMolecule molecule, int numConf)
throws BioclipseException;

@PublishedMethod(
params = "List<IMolecule> molecules",
methodSummary = "Return a list of molecules with 3D " +
"coordinates generated by Balloon.")
methodSummary = "Returns a new list of molecules with " +
"3D coordinates for the given list of " +
"molecules generated by Balloon.")
@Recorded
public List<ICDKMolecule> generateMultiple3Dcoordinates(
List<IMolecule> molecules )
Expand All @@ -176,11 +176,10 @@ public List<ICDKMolecule> generateMultiple3Dcoordinates(


@PublishedMethod(
params = "List<IMolecule> molecules, int numConf",
methodSummary = "Return a list of molecule with the " +
"selected " +
"number of target 3D " +
"conformations generated by Balloon.")
params = "List<IMolecule> molecules, int numConf",
methodSummary = "Returns a new list of molecules with numConf " +
"number of 3D conformations generated by Balloon " +
"for the molecules in the given list.")
@Recorded
public List<ICDKMolecule> generateMultiple3Dconformations(
List<IMolecule> molecules,
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